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bioRxiv · 10.64898/2025.12.11.693639

Pyranges v1: a Python framework for ultrafast sequence interval operations

Stovner, E. B.·Tico, M.·Munoz del Campo, E.·Pallares-Albanell, J.·Chawla, K.·Saetrom, P.·Mariotti, M.
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Abstract

Sequence interval algebra is key to modern bioinformatics. Pyranges v1 offers a Python Pandas-based interface to a comprehensive palette of Rust-powered operations (e.g., overlap, count, slice intervals), enabling the intuitive development of efficient pipelines for diverse sequence data, including gene annotations, mapped reads, and protein domains. Pyranges is faster, consumes less memory, and offers more functionalities than alternative tools including BEDTools, emerging as an innovative one-stop shop for omics analysis.

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Stovner, E. B., Tico, M., Munoz del Campo, E., Pallares-Albanell, J., Chawla, K., Saetrom, P., Mariotti, M.. 2025-12-12. Pyranges v1: a Python framework for ultrafast sequence interval operations. https://doi.org/10.64898/2025.12.11.693639

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